Other than reports that the Android 4.3 update has improved performance on the Nexus 7, Google seems to have addressed the performance degradation issue as well. "It appears that Google has fixed the performance degradation problem with the Nexus 7 by finally adding TRIM support in Android 4.3 (which also applies to all devices that have been upgraded, though I never had any performance issues with my Nexus 4), as noticed by Brian Klug at Anandtech. This means, in theory, that performance on the device should remain usable, even as time goes on and I continue to use my tablet to do all of the things it was designed for. I'll be watching it closely (and probably be very vocal about it if performance drops off a cliff as it did before), but I actually have a usable tablet once again, and I didn't have to shell out upwards of $200 again to get there." My Nexus 7 feels like new now that I've wiped my custom ROM and installed stock 4.3. I'm skeptical about whether or not Google has managed to solve the performance loss over time though, since it seems to be caused by low-quality NAND, and not by software.

There are two issues with root in 4.3. Keep in mind I'm very loosely paying attention as I'm waiting for the dust to clear with 4.3 before updating anything to it. So I could be off somewhere, but this is my understanding...

1) setuid is banned on the partition where su normally lives.

2) There is some role based authentication restrictions in the thread that would launch su. Which effectively limits what root can do. I kind of similar to selinux. I'm not sure if its selinux itself or not.

The two big su apps Supersu and superuser have solutions they are working on that involve a separate daemon which the lightweight su apk communicates with. Its kind of hacky, and there are a number of bugs that are still being ironed out.

I imagine ota rootkeeper is similarly affected by these same issues. You have to flash the new supersu or superuser from recovery, it can't be done from within android itself.